# config.py
import os
# LAMA 社区检测算法相关参数
ALPHA = 0.6  # PPI 网络与基因表达网络的权重比例（PPI:Expression = 0.6:0.4）
MAX_ITERATIONS = 50  # LAMA 算法的最大迭代次数
THRESHOLD = 0.5  # 社区扩展阈值

# 数据路径配置
RAW_DATA_DIR = "data/raw"
PROCESSED_DATA_DIR = "data/processed"
RESULTS_DIR = "results"

# 具体文件路径
PPI_FILES = [
    os.path.join(RAW_DATA_DIR, "ppi", "sgd_ppi.txt"),
    os.path.join(RAW_DATA_DIR, "ppi", "biogrid_ppi.txt")
]
EXPRESSION_FILES = [
    os.path.join(RAW_DATA_DIR, "gene_expression", "geo_expression.txt"),
    os.path.join(RAW_DATA_DIR, "gene_expression", "arrayexpress_expression.txt")
]

UNIFIED_PPI_FILE = os.path.join(PROCESSED_DATA_DIR, "unified_ppi.txt")
UNIFIED_EXPRESSION_FILE = os.path.join(PROCESSED_DATA_DIR, "unified_gene_expression.txt")
LAYER_MAPPING_FILE = os.path.join(PROCESSED_DATA_DIR, "layer_mapping.txt")

FUSED_NETWORK_FILE = os.path.join(PROCESSED_DATA_DIR, "fused_network.txt")

COMMUNITIES_DIR = os.path.join(RESULTS_DIR, "communities")
GO_ENRICHMENT_DIR = os.path.join(RESULTS_DIR, "go_enrichment")

# GO 富集分析配置
GO_OBO_FILE = "data/go-basic.obo"
GO_GAF_FILE = "data/goa_yeast.gaf"

# 可视化输出配置
HEATMAP_FILE = os.path.join(RESULTS_DIR, "figures", "community_similarity.png")

# 其他配置项
SEED_NODES = [813, 1234, 967]  # 示例种子节点列表（Entrez ID）